A comprehensive analysis of reassortment in influenza A virus

Genetic reassortment plays a vital role in the evolution of the influenza virus and has historically been linked with the emergence of pandemic strains. Reassortment is believed to occur when a single host - typically swine - is simultaneously infected with multiple influenza strains. The reassorted viral strains with novel gene combinations tend to easily evade the immune system in other host species, satisfying the basic requirements of a virus with pandemic potential. Therefore, it is vital to continuously monitor the genetic content of circulating influenza strains and keep an eye out for new reassortants. We present a new approach to identify reassortants from large data sets of influenza whole genome nucleotide sequences and report the results of the first ever comprehensive search for reassortants of all published influenza A genomic data. 35 of the 52 well supported candidate reassortants we found are reported here for the first time while our analysis method offers new insight that enables us to draw a more detailed picture of the origin of some of the previously reported reassortants. A disproportionately high number (13/52) of the candidate reassortants found were the result of the introduction of novel hemagglutinin and/or neuraminidase genes into a previously circulating virus. The method described in this paper may contribute towards automating the task of routinely searching for reassortants among newly sequenced strains.

Appearance of Drug Resistance-Associated Mutations in Human Immunodeficiency Virus Type 1 CRF01_AE Integrase Derived from Drug-Naive Thai Patients

CRF01_AE is a major subtype of human immunodeficiency virus type 1 (HIV-1) circulating in Southeast Asia, including Thailand. We performed genotypic studies on HIV-1 CRF01_AE integrase derived from plasma samples from drug-naive Thai patients. Direct sequencing of amplified CRF01_AE integrase genes revealed that although no primary mutations associated with drug resistance to integrase inhibitors were detected, at least one secondary mutation was found in 96% of samples. Our results indicate that the impact of these mutations on the baseline drug susceptibility of CRF01_AE viruses to integrase inhibitors may need to be addressed prior to the introduction of these drugs in Southeast Asian countries, including Thailand.

Genotypic characterization of HIV type 1 env gp160 sequences from three regions in Thailand

We report 25 env gp160 sequences from patients in three geographically distinct districts of Thailand, i.e., Lampang in the north, Trang in the south and Rayong in the east. One of these is a CRF01_AE/subtype B recombinant and the other 24 sequences are purely CRF01_AE. Very little interpopulation diversity was observed between the sequences from the three different geographic regions and from those previously reported by our laboratory from central Thailand. Potential N-linked glycosylation sites (PNLGs) were reasonably conserved among the 25 sequences: we found 15 highly conserved PNLGs on gp120 and 4 almost fully conserved PNLGs on gp41. Analysis of coreceptor tropism revealed that six of the isolates were dual tropic and the others were R5 tropic. We also examined a rare seven amino acid deletion found in one isolate at position 847-853 on gp41. These results may enhance our understanding of HIV-1 currently circulating in Thailand.

Detection of circulating Asian H5N1 viruses by a newly established monoclonal antibody

Monoclonal antibodies (MAbs) against the recently emerged Asian H5N1 virus (A/crow/Kyoto/53/2004) were generated. From five anti-hemagglutinin (HA) MAbs, four antibodies (3C11, 4C12, 3H12, and 3H4) broadly in vitro recognized and neutralized H5 subtypes, including H5N1. By contrast, the 4G6 MAb specifically reacted with H5N1-HA and not with H5N2- or H5N3-HAs from previous epidemics. The 4G6 MAb was useful for immunofluorescence assays but not for immunoblotting, suggesting that this antibody recognizes a conformational epitope of the H5N1-HA protein. An intensive epitope-mapping analysis demonstrated that the 4G6 MAb recognizes Asp59, which is highly conserved among currently circulating H5N1 lineages. Further, a 4G6-based antigen capture enzyme-linked immunosorbent assay detected H5N1 even that derived from clade 2.2 (A/chicken/Egypt/CL-61/2007) from infected chicken lung before virus isolation. Taken together, these results suggest that the established MAbs, especially 4G6, are useful for rapid and specific detection of Asian H5N1 viruses.